Molecular correlates of high B7-H3-expressing metastatic castrate-resistant prostate cancers (mCRPC) via exome, transcriptome, and epigenome analyses.
Authors: Xiaolei Shi, Abderrahman Day, Hannah E. Bergom, Sydney Tape, Sylvan Baca, Charles J. Ryan, Nick Zorko, Emmanuel S. Antonarakis, Justin Hwang
Journal: Journal of Clinical Oncology (2022)

5045 Background: mCRPC is a lethal condition with limited effective treatment options. B7-H3, a transmembrane protein of the B7 checkpoint superfamily is overexpressed in prostate cancer (PC) and is associated with poor prognosis. While several novel approaches target B7-H3 in prostate cancer, lack of knowledge about the molecular features and regulatory mechanisms of B7-H3 expression in mCRPC prevents the optimal design of these interventions. We aimed to characterize B7-H3 in mCRPC with the purpose to reveal the roles of B7-H3 in mCRPC pathogenesis, and stratify the patient population optimal for B7-H3–targeted therapies. Methods: We conducted bioinformatic interrogations at genome-scale on whole-exome and whole-transcriptome sequencing (WES, WTS) data from SU2C/PCF (n = 209, mCRPC), SUWC (n = 101, mCRPC) and GTEx (n = 246, benign prostate tissue). We developed and utilized novel machine learning (ML) algorithms to examine the association of B7-H3 with other key PC pathways. We examined the genetic and epigenetic regulation of B7-H3 by CHIP-seq. We also performed single-cell mRNA sequencing (scRNA-seq) analysis on one patient before and after treatment with the AR inhibitor, enzalutamide. We utilized both Gene Set Enrichment Analysis (GSEA) and our ML approaches to identify enriched signaling pathways in high B7-H3–expressing mCRPC. Results: Expression of B7-H3 was significantly elevated in mCRPC compared to benign prostate tissues, and was distinctive from other B7 family members. High B7-H3 expression was significantly associated with ERG fusions, AR-V7 variant, and increased FOXA1 and androgen receptor (AR) mRNA expression. At gene-level analysis, our ML algorithm suggested that B7-H3 shared similar gene networks as AR and its co-regulators, HOXB13, and FOXA1. CHIP-seq analysis revealed that the distal enhancers of B7-H3 in mCRPC were hyperactive (based on enhanced H3K27Ac marks) relative to primary tumors. Notably, these B7-H3 enhancers were bound by HOXB13, FOXA1 and AR in mCRPC samples. Our scRNA-seq analysis of one patient resistant to enzalutamide showed increased number of B7-H3-expressing cells. Based on integrated GSEA and ML analyses on WTS data, B7-H3 was positively associated with TGF-beta signaling, an enzalutamide resistance pathway. Conclusions: In mCRPC, we found B7-H3 overexpression as compared to other B7 family members. The association of B7-H3-high expression and certain genomic alterations may stratify mCRPC patients for B7-H3–targeted therapy. Further, B7-H3 exhibited regulation by AR, HOXB13 and FOXA1, at the B7-H3 enhancers. The activating epigenetic modification at the distal enhancers represents another potential marker to examine B7-H3 expression in tumors. Altogether, our study indicates that B7-H3 is a critical target in mCRPC patients, including those resistant to enzalutamide.